The code that handles the MIDI status byte checks for a match between the incoming MIDI channel and the channels for MGB (PU1, PU2, WAV, NOISE and POLY) stored in EEPROM. In any case the status byte (midiData[0]) sent to GB has its lower nibble set to 0 for PU1, 1 for PU2, 2 for WAV, 3 for NOISE and 4 for POLY.
e.g. a CC instruction for PU1, controller 1 with value 127 would send B0 01 7F